docs: def to_dict(self):
          """Return a dictionary containing Atom data."""
          data = {'aid': self.aid, 'number': self.number, 'element': self.element}
          for coord in {'x', 'y', 'z'}:
              if getattr(self, coord) is not None:
                  data[coord] = getattr(self, coord)
          if self.charge is not 0:
              data['charge'] = self.charge
          return data